7JPN
Cryo-EM structure of Arpin-bound Arp2/3 complex
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.482 |
f_angle_d | 0.538 |
f_chiral_restr | 0.045 |
f_plane_restr | 0.004 |
f_bond_d | 0.003 |
Sample |
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bovine Arp2/3 complex with Arpin |
Sample Components |
bovine Arp2/3 |
Arpin |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM CPC |
Cryogen Name | ETHANE |
Sample Vitrification Details | Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 182324 |
Reported Resolution (Å) | 3.24 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (4JD2, 1K8K) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | correlation | ||||
Overall B Value | 132 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | -1500 |
Maximum Defocus (nm) | -3500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 165000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Data were collected in super-resolution mode with an illuminated area of 1.01 um, nominal dose of 40 e-/A^2, a dose rate of 4.87 e-/s/pixel, and 2 or 5 exposures per hole by image shift. |
EM Software | ||
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Task | Software Package | Version |
IMAGE ACQUISITION | Latitude | |
CTF CORRECTION | CTFFIND | 4.1.13 |
CTF CORRECTION | cryoSPARC | 2.12.4 |
MODEL FITTING | Coot | |
INITIAL EULER ASSIGNMENT | cryoSPARC | 2.12.4 |
FINAL EULER ASSIGNMENT | cryoSPARC | 2.12.4 |
CLASSIFICATION | cryoSPARC | 2.12.4 |
RECONSTRUCTION | cryoSPARC | 2.12.4 |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction was done in cryoSPARC for intial 2D classification and then repeated in CTFFIND4 (Relion) for classification and final reconstruction. | 4485066 | Particles autopicked in cryoSPARC |